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  • CellKb Immune: a manually curated database of mammalian hematopoietic marker gene sets for rapid cell type identification.
    Ajay Patil & Ashwini Patil, bioRxiv 2020.12.01.389890; [Article]
Publications citing CellKb (18)
2024 (4)
  • A pairwise cytokine code explains the organism-wide response to sepsis.
    Michihiro Takahama, Ashwini Patil, Gabriella Richey, Denis Cipurko, Katherine Johnson, Peter Carbonetto, Madison Plaster, Surya Pandey, Katerina Cheronis, Tatsuki Ueda, Adam Gruenbaum, Tadafumi Kawamoto, Matthew Stephens & Nicolas Chevrier. Nature Immunology 25, 226–239 (2024); [Article]
  • Glomerular-tubular crosstalk via cold shock Y-box binding protein-1 in the kidney.
    Rajiv Rana, Jayakumar Manoharan, Ahmed Elwakiel, Silke Zimmermann, Jonathan A. Lindquist, Dheerendra Gupta, Moh'd Mohanad Al-Dabet, Ihsan Gadi, Jörg Fallmann, Kunal Singh, Anubhuti Gupta, Ronald Biemann, Sabine Brandt, Bekas Alo, Paul Kluge, Ravindra Garde, Christina Lamers, Khurrum Shahzad, Georg Künze, Shrey Kohli, Peter R. Mertens & Berend Isermann. Kidney International, Volume 105, Issue 1, 2024; [Article]
  • Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer.
    Anna Vyhlídalová Kotrbová, Kristína Gömöryová, Antónia Mikulová, Hana Plešingerová, Stanislava Sladeček, Marek Kravec, Šárka Hrachovinová, David Potěšil, Garett Dunsmore, Camille Blériot, Mathilde Bied, Jan Kotouček, Markéta Bednaříková, Jitka Hausnerová, Luboš Minář, Igor Crha, Michal Felsinger, Zbyněk Zdráhal, Florent Ginhoux, Vít Weinberger, Vitězslav Bryja, Vendula Pospíchalová. Journal of Extracellular Vesicles, March 2024; [Article]
  • THBS1+ myeloid cells expand in SLD hepatocellular carcinoma and contribute to immunosuppression and unfavorable prognosis through TREM1.
    Julie Giraud, Domitille Chalopin, Eloise Ramel,Thomas Boyer,Atika Zouine,Marie-Alix Derieppe,Nicolas Larmonier, Olivier Adotevi,Brigitte Le Bail, Jean-Frederic Blanc, Christophe Laurent, Laurence Chiche, Marc Derive, Macha Nikolski & Maya Saleh. Cell Reports 43 113773, Feb 2024; [Article]
2023 (8)
  • Investigating how glioblastoma tumor cells exploit their metabolic microenvironment.
    Chloe Shard, Rebecca Ormsby, Santosh Poonnoose, John Toubia, Paul Trim, Lisa Ebert, Ashwini Patil & Guillermo Gomez Neuro-Oncology, 25(Supplement_5):v274, 2023; [Article]
  • Commensal bacteria promote type I interferon signaling to maintain immune tolerance in mice.
    Adriana Vasquez Ayala, Chia-Yun Hsu, Renee E. Oles, Kazuhiko Matsuo, Luke R. Loomis, Ekaterina Buzun, Marvic Carrillo Terrazas, Romana R. Gerner, Hsueh-Han Lu, Sohee Kim, Ziyue Zhang, Jong Hwee Park, Paul Rivaud, Matt Thomson, Li-Fan Lu, Booki Min, Hiutung Chu. Journal of Experimental Medicine Dec 2023; [Article]
  • Glycolytic shift during West Nile virus infection provides new therapeutic opportunities.
    Patricia Mingo-Casas, Ana-Belén Blázquez, Marta Gómez de Cedrón, Ana San-Félix, Susana Molina, Estela Escribano-Romero, Eva Calvo-Pinilla, Nereida Jiménez de Oya, Ana Ramírez de Molina, Juan-Carlos Saiz, María-Jesús Pérez-Pérez & Miguel A. Martín-Acebes. Journal of Neuroinflammation 20, 217(2023); [Article]
  • Integrated multi-omics analysis reveals insights into Chinese forest musk deer (Moschus berezovskii) genome evolution and musk synthesis.
    Feng H, Feng T, Mo Y, Sun S, Wang L, Lu C, Feng C, Xing K & Su Z. Frontiers in Cell and Development Biology. 11:1156138; [Article]
  • Metformin suppresses calcium oxalate crystal-induced kidney injury by promoting Sirt1 and M2 macrophage-mediated anti-inflammatory activation.
    .Haoran Liu, Chen Duan, Xiaoqi Yang, Jianhe Liu, Yaoliang Deng, Hans-Göran Tiselius, Zhangqun Ye, Tao Wang, Jinchun Xing & Hua Xu. Signal Transduction and Targeted Therapy 8, 38 (2023); [Article]
  • Tumor Microenvironment and Genes Affecting the Prognosis of Temozolomide-Treated Glioblastoma.
    Jang Y, Cheong W, Park G, Kim Y, Ha J & Ahn S. Journal of Personalized Medicine. 2023; 13(2):188; [Article]
  • Determinants of renin cell differentiation: a single cell epi-transcriptomics approach.
    Alexandre G Martini, Jason P. Smith, Silvia Medrano, Nathan C. Sheffield, Maria Luisa S. Sequeira-Lopez & R. Ariel Gomez. bioRxiv 2023.01.18.524595; [Article]
  • Publication, Funding, and Experimental Data in Support of Human Reference Atlas Construction and Usage.
    Yongxin Kong & Katy Börner. bioRxiv 2023.10.21.563417; [Article]
2022 (4)
  • Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging.
    Christa Haase, Karin Gustafsson, Shenglin Mei, Shu-Chi Yeh, Dmitry Richter, Jelena Milosevic, Raphaël Turcotte, Peter V. Kharchenko, David B. Sykes, David T. Scadden & Charles P. Lin. Nature Methods 19, 1622–1633 (2022); [Article]
  • WebCSEA: web-based cell-type-specific enrichment analysis of genes.
    Yulin Dai, Ruifeng Hu, Andi Liu, Kyung Serk Cho, Astrid Marilyn Manuel, Xiaoyang Li, Xianjun Dong, Peilin Jia & Zhongming Zhao. Nucleic Acids Research, Volume 50, Issue W1, 5 July 2022; [Article]
  • Tetrabromobisphenol A effects on differentiating mouse embryonic stem cells reveals unexpected impact on immune system.
    Tribondeau Alicia, Sachs Laurent M & Buisine Nicolas. Frontiers in Genetics, VOLUME=13, YEAR=2022; [Article]
  • Tumor-associated macrophages are shaped by intratumoral high potassium via Kir2.1
    Sheng Chen, Wenyu Cui, Zhexu Chi, Qian Xiao, Tianyi Hu, Qizhen Ye, Kaixiang Zhu, Weiwei Yu, Zhen Wang, Chenxuan Yu, Xiang Pan, Siqi Dai, Qi Yang, Jiacheng Jin, Jian Zhang, Mobai Li, Dehang Yang, Qianzhou Yu, Quanquan Wang, Xiafei Yu, Wei Yang, Xue Zhang, Junbin Qian, Kefeng Ding & Di Wang. Cell Metabolism 34, 1843–1859, November 1, 2022; [Article]
2021 (1)
  • A deep convolutional neural network for segmentation of whole-slide pathology images identifies novel tumour cell-perivascular niche interactions that are associated with poor survival in glioblastoma.
    Amin Zadeh Shirazi, Mark D. McDonnell, Eric Fornaciari, Narjes Sadat Bagherian, Kaitlin G. Scheer, Michael S. Samuel, Mahdi Yaghoobi, Rebecca J. Ormsby, Santosh Poonnoose, Damon J. Tumes & Guillermo A. Gomez. British Journal of Cancer 125, 337–350 (2021); [Article]
2020 (1)
  • Unsupervised Identification of SARS-CoV-2 Target Cell Groups via Nonlinear Dimensionality Reduction on Single-cell RNA-Seq Data.
    Saiteja Danda, Akram Vasighizaker & Luis Rueda. IEEE International Conference on Bioinformatics and Biomedicine (BIBM); [Article]